Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 311 Profile

GeneModule member RegulatorRegulator MotifMotif
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 311

There are 11 regulatory influences for Module 311

Regulator Table (11)
Regulator Name Type
DVU2675 tf
DVU0309
DVU0596
combiner
DVU1967 tf
DVU2557
DVU2675
combiner
DVU0309
DVU3305
combiner
DVUA0151 tf
DVU0309
DVU0744
combiner
DVU0309
DVU1967
combiner
DVU0309
DVU0621
combiner
DVU2690 tf
DVU0309
DVU0529
combiner

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (2)
Motif Id e-value Consensus Motif Logo RegPredict
595 3.00e+00 ATgtGcAAAA
Loader icon
RegPredict
596 8.00e-01 aTGccGtCAT
Loader icon
RegPredict
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment

Regulon 311 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Fatty acid biosynthesis kegg pathway 2.00e-06 7.10e-05 3/32
Lipid Metabolism kegg subcategory 3.90e-05 7.61e-04 4/32
Cell Motility kegg subcategory 1.32e-02 4.26e-02 3/32
Lipid Metabolism kegg subcategory 3.11e-04 3.46e-03 3/32
Fatty acid biosynthesis kegg pathway 2.00e-06 6.90e-05 3/32
Cellular Processes kegg category 8.55e-03 2.38e-02 3/32
Cell Motility kegg subcategory 8.55e-03 2.38e-02 3/32

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 2.66e-02 3.67e-02 3/32
regulation of transcription, DNA-dependent biological_process 3.73e-02 4.97e-02 4/32
chemotaxis biological_process 8.10e-05 3.97e-04 4/32
two-component sensor activity molecular_function 4.48e-03 7.41e-03 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methyl-accepting chemotaxis protein cog 7.60e-05 1.07e-04 3/32
Cell motility cog subcategory 1.66e-03 2.28e-02 4/32
Signal transduction mechanisms cog subcategory 2.41e-02 3.86e-02 5/32
Cell motility cog subcategory 1.66e-03 3.14e-03 4/32
Methyl-accepting chemotaxis protein cog 7.60e-05 1.96e-04 3/32
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Members for Module 311

There are 32 genes in Module 311

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0030 CDS 2793310 chromosome 36482 37984 - GntR family transcriptional regulator True
DVU0108 CDS 2793307 chromosome 140811 140918 - hypothetical protein DVU0108 False
DVU0109 CDS 2793308 chromosome 141455 142687 + sensor histidine kinase False
DVU0172 CDS 2795602 chromosome 215484 216485 - iron-sulfur cluster-binding protein False
DVU0173 CDS 2795603 chromosome 216495 218696 - thiosulfate reductase False
DVU0186 CDS 2795711 chromosome 230021 230800 + hypothetical protein DVU0186 False
DVU0622 CDS 2796146 chromosome 688231 690729 - sensor histidine kinase/response regulator False
DVU0750 CDS 2794968 chromosome 840322 842331 - methyl-accepting chemotaxis protein False
DVU1168 CDS 2794856 chromosome 1260521 1260937 - hypothetical protein DVU1168 False
DVU1169 CDS 2794857 chromosome 1261035 1263449 - methyl-accepting chemotaxis protein False
DVU1445 CDS 2794572 chromosome 1522387 1523982 - flagellar hook-length control domain-containing protein False
DVU1960 cheA-2 CDS 2793473 chromosome 2035941 2038034 - chemotaxis protein CheA False
DVU2110 CDS 2793382 chromosome 2204660 2206297 - L-lactate permease False
DVU2195 CDS 2795763 chromosome 2291911 2292168 + hypothetical protein DVU2195 True
DVU2294 CDS 2795448 chromosome 2385828 2386907 - femAB family protein False
DVU2317 CDS 2795277 chromosome 2411334 2413103 + methyl-accepting chemotaxis protein False
DVU2560 CDS 2796134 chromosome 2672449 2672835 + hypothetical protein DVU2560 False
DVU2561 CDS 2796254 chromosome 2672832 2673860 + short chain dehydrogenase/reductase family oxidoreductase False
DVU2562 CDS 2796255 chromosome 2673960 2674367 + acyl carrier protein False
DVU2563 CDS 2796256 chromosome 2674645 2676093 + beta-ketoacyl synthase False
DVU2565 bioD CDS 2796258 chromosome 2677915 2678655 + dethiobiotin synthetase False
DVU2566 lysA-2 CDS 2796259 chromosome 2678811 2680076 - diaminopimelate decarboxylase False
DVU2802 CDS 2795388 chromosome 2904939 2905634 + GntR family transcriptional regulator True
DVU2803 CDS 2795389 chromosome 2905914 2907323 + hypothetical protein DVU2803 False
DVU2805 CDS 2793766 chromosome 2908544 2910490 + P47K family cobalamin synthesis protein False
DVU2806 CDS 2793767 chromosome 2910477 2911226 + MotA/TolQ/ExbB proton channel family protein False
DVU2807 CDS 2793768 chromosome 2911246 2911656 + biopolymer ExbD/TolR family transporter False
DVU3284 CDS 2796008 chromosome 3459535 3461166 - L-lactate permease False
DVU3290 CDS 2796014 chromosome 3464277 3465332 + hypothetical protein DVU3290 False
DVU3291 CDS 2796015 chromosome 3465296 3466930 + glutamate synthase, iron-sulfur cluster-binding subunit False
DVU3312 CDS 2796048 chromosome 3488692 3489147 + hypothetical protein DVU3312 False
DVU3372 CDS 2795686 chromosome 3544779 3544910 - hypothetical protein DVU3372 False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.